Biochip detection system

ABSTRACT

A biochip detection system detects and locates samples that are labeled with multiple fluorescent tags and are located on a biochip. This biochip detection system includes a charge coupled device (CCD) sensor, a broad spectrum light source, a lens, a light source filter, and a sensor filter. The CCD sensor comprises two dimensional CCD arrays to simultaneously detect light waves from at least a substantial portion of the biochip. The broad spectrum light source is optically coupled to the CCD sensor and is configured to be utilized with a variety of different fluorescent tags which have differing excitation wavelengths.  
     The lens and the CCD sensor are optimized and matched to each other such that the sensor operates at or below the diffraction rating of the lens. Further, the resolution of the CCD sensor is matched to the samples on the biochip such that the CCD sensor oversamples each of the samples a sufficient number of times. Additionally, the lens is configured to frame at least a substantial portion of the biochip.  
     The biochip detection system is optimized to provide a higher dynamic range, increased sensitivity, and faster throughput compared to system utilizing laser scanners. Further, the biochip detection system is capable of utilizing a same broad spectrum light source to excite samples labeled with a variety of fluorescent tags.

FIELD OF THE INVENTION

[0001] The invention relates to the field of detectors for analysis ofbiological samples located on biochips. More particularly, the inventionrelates to the field of detectors that analyze samples labeled with atag while utilizing a charge coupled device sensor.

BACKGROUND OF THE INVENTION

[0002] Detection devices that detect and locate samples contained on abiochip via laser light sources and laser scanners are well known in theart. These detection devices require that the samples be labeled by afluorescent tag. Typically, these detection devices rely on laser lightsources to excite the samples that are labeled by a fluorescent tag andcauses biologically active samples to output emitted light waves. Thelaser source is scanned to serially excite each sample on the biochip todetect any emitted light waves from the samples that are biologicallyactive.

[0003] Unfortunately, these detection devices utilizing either the laserlight source or the laser scanner suffer from various drawbacks. First,laser scanners utilized to detect the emitted light waves from theexited samples on the biochip typically require wait times upwards offive minutes for sufficient resolution. Because laser scanners operateas a serial scanning device by sequentially detecting one sample at atime on the surface of the biochip, laser scanners are inherentlyinefficient at detecting the emitted light waves from an array ofsamples.

[0004] Further, laser light sources utilized within the detectiondevices inherently only emit coherent light waves which span over anextremely narrow range of wavelengths. Fluorescent tags are generallyresponsive to a single frequency of light or light from a narrowfrequency band. Thus, the use of the laser light sources severely limitsthe flexibility of those detection devices because only one type offluorescent tag can be used. To use other tags, additional laser sourcesmust be used. Further, to evaluate a biochip that has been treated withmultiple tags, the prior art's long duration scan cycle must beperformed for each one of the required laser sources.

[0005] For example, if samples on a biochip were labeled with twodifferent fluorescent tags and the different tags required light waveswith substantially different excitation wavelengths, analyzing thesesamples would require the user to change laser light sources theanalysis of all the samples were completed. Additionally, to be able tohandle samples labeled with different fluorescent tags with differingexcitation wavelengths, the user is required to have access to a varietyof laser light sources. Since laser light sources are costly andspecialized items, there are substantial costs and inconveniencesassociated with utilizing these prior detection devices.

[0006] Therefore, it is desirable to have an ability to detect andlocate samples labeled with multiple tags contained on a biochip,without the need for a laser light source. It is also desirable have anability to detect and locate samples labeled with a tag contained on abiochip, without the need for a serial scanning device.

SUMMARY OF THE INVENTION

[0007] The invention is a biochip detection system for detecting andlocating samples that are labeled with multiple tags and are located ona biochip. This biochip detection system includes a charge coupleddevice (CCD) sensor, a broad spectrum light source, a lens, a lightsource filter, and a sensor filter. The CCD sensor comprises twodimensional CCD arrays to simultaneously detect light waves from atleast a substantial portion of the biochip. The broad spectrum lightsource is optically coupled to the CCD sensor and is configured to beutilized with a variety of different fluorescent tags which havediffering excitation wavelengths.

[0008] The light source filter is optically coupled between the lightsource and the biochip and is configured to only substantially allowlight waves that have an excitation wavelength corresponding to aparticular fluorescent tag to reach the biochip. The light source filterprevents light waves that have similar wavelengths to an emissionwavelength of the particular fluorescent tag from reaching the biochipor the CCD sensor. The sensor filter is optically coupled between thebiochip and the CCD sensor and is configured to only substantially allowlight waves that have the emission wavelength corresponding to thefluorescent tag to reach the CCD sensor. The sensor filter preventsextraneous light waves from giving the CCD sensor false signals.

[0009] The lens and the CCD sensor are optimized and matched to eachother such that the sensor operates at or below the diffraction ratingof the lens. Further, the resolution of the CCD sensor is matched to thesamples on the biochip such that the CCD sensor oversamples each of thesamples a sufficient number of times. Additionally, the lens isconfigured to frame at least a substantial portion of the biochip.

[0010] The biochip detection system is optimized to provide a higherdynamic range, increased sensitivity, and faster throughput compared tosystem utilizing laser scanners. Further, the biochip detection systemis capable of utilizing a same broad spectrum light source to excitesamples labeled with a variety of fluorescent tags.

BRIEF DESCRIPTION OF THE DRAWINGS

[0011]FIG. 1 illustrates a schematic side view of internal elements ofthe preferred embodiment of the present invention.

[0012]FIG. 2 illustrates a schematic side view of the preferredembodiment configured to analyze two sets of samples on a single biochipwith each set of samples labeled with a different fluorescent tag.

[0013]FIG. 3 illustrates a schematic side view of the preferredembodiment configured to analyze a plurality of samples on a singlebiochip with the plurality of samples labeled with multiple fluorescenttags.

[0014]FIG. 4 is a graph that illustrates a relationship between a lightintensity versus a wavelength of an excitation light of a particularfluorescent tag, an emitted light of this particular fluorescent tag,and the source light as utilized in the present invention.

[0015]FIG. 5 illustrates a top view of an external housing of analternate embodiment.

[0016]FIG. 6 illustrates a side view of the external housing of thealternate embodiment.

[0017]FIG. 7 illustrates a perspective view of the external housing ofthe alternate embodiment.

[0018]FIG. 8 illustrates a side view of a camera housing of thepreferred embodiment.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

[0019]FIG. 1 illustrates a side view of the preferred embodiment of thepresent invention. This preferred embodiment is a biochip detectionsystem 100 as shown in FIG. 1. The biochip detection system 100preferably includes a lens 120, a sensor filter 130, a charge coupleddevice (CCD) sensor 140, a light source 150, and a light source filter160. Preferably, the biochip detection system 100 is configured todetect and locate samples 110 within a biochip 170. The samples 110 andthe biochip 170 are shown for exemplary purposes only and are notintended to be part of the present invention. For the purposes of thisspecification, the biochip 170 is configured to have an array of samples110 arranged in a predetermined number of rows and columns on top of asubstrate. Further, the samples 110 contained within the biochip 170 arecapable of including DNA or other biological material. For the biochipdetection system 100 to properly operate, the samples 110 are labeledwith a tag. The biochip 170 in the preferred embodiment is configured tohold samples 110 which are labeled with multiple tags. However, it willbe apparent to those skilled in the art to utilize samples 110 onlylabeled by one tag on the biochip 170. The samples 110 in the preferredembodiment are labeled with a fluorescent tag. However, it will beapparent to those skilled in the art to substitute this fluorescent tagwith a chemiluminescent tag, colormetric tag, or the like. The processof labeling samples with a tag is well known in the art.

[0020] The biochip detection system 100 detects and locates which onesof the plurality of samples 110 are fluorescently labeled within thebiochip 170. The biochip detection system 100 operates by exciting thesamples 110 labeled by a fluorescent tag with light waves having anexcitation wavelength thereby generating samples 110 that emit lightwaves having an emitted wavelength. Next, the CCD sensor 140simultaneously detects the light waves having the emitted wavelengthfrom at least a portion of the biochip 170. Specific elements andprocedures of the biochip detection system 100 are described in detailbelow.

[0021] The CCD sensor 140 is preferably configured to include a twodimensional array of charge coupled devices. Preferably by having theCCD sensor 140 as a two dimensional sensor, the biochip detection system100 is capable of simultaneously imaging either an entire area or aportion of the biochip 170 (depending on the size of the biochip 170)for light waves emitted by the samples 110. By simultaneously imagingall the biochip 170, the CCD sensor 140 allows the biochip detectionsystem 100 to complete the detection process in most cases well underone minute and in some cases in twenty-five seconds. In an alternateembodiment, the CCD sensor 140 comprises cooled charge coupled devices.By having the charge coupled devices within the CCD sensor 140 cooled,background noise is reduced and signal clarity is maximized. In thispreferred embodiment, the CCD sensor 140 is manufactured by SonyCorporation having the model number ICX 038DLA. It will be apparent tothose skilled in the art to utilize a different CCD sensor 140.

[0022] The light source 150 is preferably a broad spectrum bulb that isconfigured to output light waves over a wide range of wavelengths.Preferably, the light source 150 is optically coupled to the biochip170. Because the light source 150 generates light waves over a widerange of wavelengths, the light source 150 is capable of forming lightwaves to excite samples labeled with a wide variety of fluorescent tags.In this preferred embodiment, the light source 150 is manufactured byGeneral Electric Corporation having the model number 150 Watt EKE. Itwill be apparent to those skilled in the art to select a different lightsource.

[0023] The lens 120 is preferably a compound lens that includes multiplelens elements. The lens 120 is located in an optical path between thebiochip 170 and the CCD sensor 140. Preferably, the lens 120 transmitslight waves emitted from the samples 110 to the CCD sensor 140. The lens120 is capable of adjusting and optimizing a magnification parametersuch that a desired portion of the biochip 170 is captured by the CCDsensor 140 with an appropriate field of view. Preferably, the lens 120is configured such that the CCD sensor 140 operates at or below thediffraction limit of the lens 120. In this preferred embodiment, thelens 120 is manufactured by Fujinon having a focal length of 25millimeters and f-stop of 1:0.85. It will be apparent to those skilledin the art that the lens 120 can be substituted for a different lens ormultiple lenses.

[0024] Preferably, the light source filter 160 is optically coupledbetween the light source 150 and the biochip 170. The light sourcefilter 160 is preferably configured to substantially only allow lightwaves generated by the light source 150 with a predetermined excitationwavelength to reach the biochip 170. The predetermined excitationwavelength corresponds to a particular wavelength that excites one ofthe samples 110 that is labeled with a particular fluorescent tag. Thepredetermined excitation wavelength depends on the sample in conjunctionwith the fluorescent tag. In other words, the light source filter 160substantially blocks all light waves from the light source 150 withwavelengths other than the predetermined excitation wavelength fromreaching the biochip 170. By blocking substantially all light waves thathave wavelengths other than the predetermined excitation wavelength, thelight source filter 160 prevents erroneous light waves generated by thelight source 150 from giving the CCD sensor 140 erroneous signals.

[0025] Preferably, the sensor filter 130 is optically coupled betweenthe CCD sensor 140 and the biochip 170. As shown in FIG. 1, the sensorfilter 130 is preferably between the CCD sensor 140 and the lens 120. Byplacing the sensor filter 130 between the lens 120 and the CCD sensor140, the chances of distorting the light waves for detection by the CCDsensor 140 is minimized. Nevertheless, it will be apparent to thoseskilled in the art that the sensor filter 130 also can be configuredbetween the lens 120 and the biochip 170. The sensor filter 130 ispreferably configured to substantially only allow light waves that areemitted from a sample labeled with a particular fluorescent tag that hasa predetermined emitted wavelength to reach the CCD sensor 140. Thepredetermined emitted wavelength occurs during excitation of this sampleand depends on the sample in conjunction with the particular fluorescenttag. Preferably, the sensor filter 130 is optimized to parameters of thelight source 150 and prevents extraneous light waves from reaching theCCD sensor 140 thereby increasing the accuracy and sensitivity of thebiochip detection system 100. It will be apparent to those of ordinaryskill in the art that the filter selection is made to correspond withthe fluorescent tags and also the sample type.

[0026] The biochip detection system 100 is capable of efficientlydetecting and locating samples 110 on the biochip 170. The CCD sensor140 and the lens 120 are preferably optimized relative to each other andalso to the samples 110 on the biochip 170. In particular, the CCDsensor 140 preferably has a transmission resolution to oversample eachof the samples 110 by eight to nine times. For example, the CCD sensor140 is preferably configured to have each of the samples 110 beoptically detected by eight to nine pixels. Additionally, the lens 120is preferably optimized to allow the CCD sensor 140 to operate at orbelow the diffraction limit of the lens 120.

[0027] In operation, the biochip detection system 100 is preferablyconfigured to analyze the biochip 170. The samples 110 are containedwithin the biochip 170 and are labeled with a multiple fluorescent tags.The biochip detection system 100 initiates operation by activating thelight source 150. The light waves emitted from the light source 150 arerepresented with a light wave 180 in FIG. 1. Next, the light wave 180preferably passes through the light source filter 160. As the light wave180 passes through the filter, some wavelengths of the light wave 180are blocked. A resultant light wave after passage through the lightsource filter 160 is represented as a light wave 190 as shown in FIG. 1.Preferably, the light wave 190 only substantially includes light waveswith a predetermined excitation wavelength which correspondingly excitesthe samples 110 which are labeled with the particular fluorescent tag.

[0028] As the samples 110 are excited by the predetermined excitationwavelength in the light wave 190, the samples 110 produce light waveswhich are represented by a light wave 200 as shown in FIG. 1. The lightwave 200 preferably includes light waves with a predetermined emissionwavelength which are produced by the samples 110. The light wave 200then passes through the lens 120. Some extraneous light waves with thepredetermined excitation wavelength also pass through the lens 120 asshown by the light wave 190. Next, the sensor filter 130 preferablyblocks out substantially all light waves with wavelengths other than thepredetermined emission wavelength; the sensor filter 130 substantiallyonly allows light waves represented by the light wave 200 to reach theCCD sensor 140. By substantially allowing only light waves having thepredetermined emission wavelength to reach the CCD sensor 140, the CCDsensor 140 is capable of accurately detecting and locating the samples110 on the biochip 170. As a result, the CCD sensor 140 is preventedfrom erroneously detecting stray light waves.

[0029] The biochip detection system 100 is capable of accommodating avariety of fluorescent tags without switching the light source 150, thelens 120, or the CCD sensor 140. To utilize multiple fluorescent tagswith the biochip detection system 100, only the light source filter 160and the emission filter 130 are preferably changed. By merely changingthe light source filter 160 and the sensor filter 130, the biochipdetection system 100 is capable of detecting and locating the sampleslabeled by this new fluorescent tag. Preferably, the light source filter160 is changed such that substantially only light waves with anexcitation wavelength corresponding to a new fluorescent tag reach thesamples labeled by this new fluorescent tag. Further, the sensor filter130 is preferably changed such that substantially only light waves withan emission wavelength corresponding to the new fluorescent tag reachthe CCD sensor 140.

[0030]FIG. 2 illustrates the biochip detection system 100 configured toanalyze a biochip 210 having two sets of samples with each set ofsamples labeled by a different fluorescent tag. The configuration of thebiochip detection system 100 which includes the light source 150, thelens 120, the sensor filters 130 and 130′, the light source filters 160and 160′, and the CCD sensor 140 is similar to the biochip detectionsystem 100 in FIG. 1. The sensor filters 130 and 130′ are usedinterchangeably, one each for detecting the presence of differentfluorescent tags. The light source filters 160 and 160′ are usedinterchangeably to illuminate the biochip 210 with different wavelengthsof light. It will be apparent to those skilled in the art thatadditional filters can be utilized. The biochip 210 contains a first setof samples 220 which is labeled by a first fluorescent tag, and a secondset of samples 230 which is labeled by a second fluorescent tag. First,the biochip detection system 100 is configured to locate and detect thefirst set of samples 220. For proper configuration to detect and locatethe first set of samples 220, the source light filter 160 preferablysubstantially only allows light waves with an excitation wavelengthcorresponding to the first fluorescent tag to reach the biochip 210.Further, the sensor filter 130 preferably substantially only allowslight waves with an emission wavelength corresponding to the firstfluorescent tag to reach the CCD sensor 140.

[0031] After the biochip detection system 100 is finished detecting andlocating the first set of samples 220, the system 100 is configured todetect and locate the second set of samples 230. For properconfiguration to detect and locate the second set of samples 230, thesource light filter 160′ preferably substantially only allows lightwaves with an excitation wavelength corresponding to the secondfluorescent tag to reach the biochip 210. Further, the sensor filter130′ preferably substantially only allows light waves with an emissionwavelength corresponding to the second fluorescent tag to reach the CCDsensor 140. The filter can be manually changed. For systems used toroutinely tests samples labeled with several known fluorescent tags, thefilters can be automatically interchanged, for example, using aso-called “jukebox”. Although the first set of samples 220 and thesecond set of samples 230 are described as being labeled with afluorescent tag, it will be apparent to those skilled in the art tosubstitute a fluorescent tag with a chemiluminescent tag, colormetrictag, and the like.

[0032]FIG. 3 illustrates the biochip detection system 100 configured toanalyze a biochip 700 having a plurality of samples 710 wherein each ofthe plurality of samples 710 are preferably labeled by multiplefluorescent tags. The configuration of the biochip detection system 100which includes the light source 150, the lens 120, the sensor filters130 and 130′, the light source filters 160 and 160′, and the CCD sensor140 remain identical to the biochip detection system 100 in FIG. 2. Thesensor filters 130 and 130′ are used interchangeably, one each fordetecting the presence of different fluorescent tags. The light sourcefilters 160 and 160′ are used interchangeably to illuminate the biochip700 with different wavelengths of light. It will be apparent to thoseskilled in the art that additional filters can be utilized. Theplurality of samples 710 are represented as being labeled by a firstfluorescent tag 720 and a second fluorescent tag 730. It will beapparent to those with ordinary skill in the art to label the pluralityof samples 710 with any number of tags.

[0033] First, the biochip detection system 100 is configured to locateand detect the plurality of samples 710 that are labeled with the firstfluorescent tag 720. For proper configuration to detect and locate theplurality of samples 710 that are labeled with the first fluorescent tag720, the source light filter 160 preferably substantially only allowslight waves with an excitation wavelength corresponding to the firstfluorescent tag to reach the biochip 700. Further, the sensor filter 130preferably substantially only allows light waves with an emissionwavelength corresponding to the first fluorescent tag 720 to reach theCCD sensor 140.

[0034] After the biochip detection system 100 is finished detecting andlocating the plurality of samples 710 that are labeled with the firstfluorescent tag 720, the system 100 is configured to detect and locatethe plurality of samples 710 that are labeled with the secondfluorescent tag 730. For proper configuration to detect and locate theplurality of samples 710 that are labeled with the second fluorescenttag 730, the source light filter 160′ preferably substantially onlyallows light waves with an excitation wavelength corresponding to thesecond fluorescent tag 730 to reach the biochip 700. Further, the sensorfilter 130′ preferably substantially only allows light waves with anemission wavelength corresponding to the second fluorescent tag 730 toreach the CCD sensor 140. The filter can be manually changed. Forsystems used to routinely tests samples labeled with several knownfluorescent tags, the filters can be automatically interchanged, forexample, using a so-called “jukebox”. Although the plurality of samples710 are described as being labeled with multiple fluorescent tags, itwill be apparent to those skilled in the art to substitute multiplefluorescent tags with multiple chemiluminescent tags, colormetric tags,and the like.

[0035]FIG. 4 illustrates a graph representing intensity of light alongthe vertical axis and wavelength along the horizontal axis. A curve 300is representative of the light output from the light source 150 (FIGS.1, 2, and 3). As observed from the curve 300, the light source 150outputs light waves preferably at an uniform intensity over a range ofwavelengths. A curve 310 is centered around λ_(Excited) and represents adesired light intensity and wavelength to strike a sample labeled with aparticular fluorescent tag in order to excite this sample. A curve 320is centered around λ_(Emitted) and represents an emitted light intensityand wavelength from this sample while this sample is excited by lightwaves represented by the curve 310.

[0036] The curves 300, 310, and 320 illustrate the functions of thelight source filter 160 and the sensor filter 130 as illustrated inFIGS. 1, 2, and 3 and as described above. For example, while inoperation, the light source 150 preferably outputs light wavesrepresented by the curve 300. Preferably, the light source filter 160substantially only allows light waves that have wavelengths centeredaround the λ_(Excited) to reach the sample labeled by this particularfluorescent tag. Consequently, these light waves that have wavelengthscentered around the λ_(Excited) excite the sample and are represented bythe curve 310. While excited, this sample preferably emits light wavesthat have wavelengths centered around the λ_(Emitted). Preferably, thesensor filter 130 substantially only allows light waves that havewavelengths centered around the λ_(Emitted) (which are represented bythe curve 320) to reach the CCD sensor 140.

[0037] By having the source light filter 160 prevent light waves thathave wavelengths centered around the λ_(Emitted) from striking thissample, the source light filter 160 prevents erroneous light waves frompassing through the sensor filter 130 and striking the CCD sensor 140.Further, by having the sensor filter 130 prevent light waves that havewavelengths centered around the λ_(Excited) from passing through thebiochip 170 and then striking the CCD sensor 140, the sensor filter 130prevents erroneous readings from the CCD sensor 140. As a result of thesource light filter 160 and the sensor filter 130, fewer or no stray,erroneous light waves strike the CCD sensor 140.

[0038]FIG. 5 illustrates an external top view of an alternate embodimentof the biochip detection system 100. A main housing 400 is configured tohold the biochip 170 and the light source 150. The main housing 400 isalso configured to be light proof. By being light proof, the mainhousing 400 prevents extraneous light waves from giving the CCD sensor140 erroneous signals. At least one articulating mirror 410 is utilizedwithin the main housing 400 for appropriately directing light waves fromthe light source 150 to the biochip 170. A camera housing 420 isutilized to hold the CCD sensor 140 and coupled to the main housing 400.

[0039]FIG. 6 illustrates an external side view of the alternateembodiment of the biochip detection system 100. The main housing 400includes a drawer 440 which allows a user to change the biochip 170,adjust the light source filter 160, and/or adjust the light source 150.The drawer 440 includes appropriate seals to engage the main housing 400such that the main housing 400 remains light proof. A filter box 480 iscoupled to the main housing 400. The filter box 480 is configured tosecurely hold the sensor filter 130 and has an opening 450 to accept thesensor filter 130. The camera housing 420 is mounted to the filter box480 via a camera mounting bracket 430. Preferably, a light shield 510 ismounted between the camera housing 420 and the filter box 480 to preventstray light waves from entering either the camera housing 420, the mainhousing 400, or the filter box 480.

[0040]FIG. 7 illustrates an external perspective view of the alternateembodiment of the biochip detection system 100. For the sake of clarity,the camera housing 420, the camera mounting bracket 430, and the lightshield 510 are omitted from FIG. 6. A fiber optic port 490 is providedin the main housing 400. The fiber optic port 490 allows the biochipdetection system 100 to interface with an external light source which iscapable of transmitting light via a fiber optic cable connected to theexternal light and the fiber optic port 490. The filter box 480 has alight channel 530 for allowing light to pass through the filter box 480from the main housing 400 to the camera housing 420. Further, the filterbox 480 also has an opening 505 to accept a ball plunger 500. A filterholder 460 is configured to hold at least one sensor filter 130 and hasa plurality of notches 520. The filter holder 460 is configured to slidethrough the opening 450 in the filter box 480. The ball plunger 500 isconfigured to engage one of the plurality of notches 520 toappropriately position the filter holder 460 relative to the filter box480.

[0041] A preferred embodiment of the external housing is similar to thealternate embodiment as shown in FIGS. 5, 6, and 7. A main differencebetween the alternate embodiment and the preferred embodiment is thatthe preferred embodiment does not utilize the filter box 480 and thefilter holder 460 as shown in FIGS. 5, 6, and 7. Instead, the preferredembodiment of the external housing preferably couples the camera mountbracket 430 directly to the main housing 400. Further, the camerahousing 420 as shown in FIGS. 5 and 6 is modified and replaced in thepreferred embodiment by a camera housing 600. The camera housing 600 isillustrated in FIG. 8. Unlike the alternate embodiment of the camerahousing 420 (FIGS. 5 and 6), the camera housing 600 preferably containsa filter wheel 610 which holds at least one sensor filter 130.Preferably, the filter wheel 610 optically couples the sensor filter 130between the lens 120 and the CCD sensor 140. Further, the filter wheel610 is preferably configured to change positions thus allowing differentsensor filters 130 to be optically coupled between the lens 120 and theCCD sensor 140.

[0042] The present invention has been described in terms of specificembodiments incorporating details to facilitate the understanding of theprinciples of construction and operation of the invention. Suchreference herein to specific embodiments and details thereof is notintended to limit the scope of the claims appended hereto. It will beapparent to those skilled in the art that modifications can be made inthe embodiments chosen for illustration without departing from thespirit and scope of the invention.

[0043] Specifically, it will be apparent to one of ordinary skill in theart that the device of the present invention could be implemented inseveral different ways and the apparatus disclosed above is onlyillustrative of the preferred embodiment of the invention and is in noway a limitation. For example, it would be within the scope of theinvention to vary the dimensions disclosed herein. In addition, it willbe apparent that the various aspects of the above-described inventioncan be utilized singly or in combination with one or more of the otheraspects of the invention described herein. In addition, the variouselements of the present invention could be substituted with otherelements.

What is claimed is:
 1. An apparatus configured for analyzing a sample,the apparatus comprising: a. a sensor configured for detecting emittedlight from the sample; b. a light source optically coupled to the sensorconfigured to illuminate the sample with an excitation light having afirst wavelength; and c. a matched filter optically coupled between thesample and the sensor for allowing substantially only the emitted lighthaving a second wavelength to pass therethrough and strike the sensor.2. The apparatus according to claim 1 wherein the sensor is a chargecoupled device.
 3. The apparatus according to claim 1 wherein the sensoris a two dimensional charge coupled device.
 4. The apparatus accordingto claim 1 wherein the light source is a coherent light source such as alaser.
 5. The apparatus according to claim 1 wherein the light source isa broad spectrum light source and the apparatus further comprising asecondary filter located between the broad spectrum light source and thesample such that substantially only the excitation light with the firstwavelength reaches the sample.
 6. The apparatus according to claim 1further comprising a lens optically coupled between the sample and thesensor for focussing the emitted light.
 7. An apparatus configured foranalyzing a biochip containing a tag labeled sample, the apparatuscomprising a. a two dimensional CCD sensor for detecting emitted lightfrom the tag labeled sample on the biochip; and b. a lens opticallycoupled between the two dimensional CCD sensor and the biochip andconfigured to transmit the emitted light to the two dimensional CCDsensor wherein the lens is configured to be within two inches of the taglabeled sample.
 8. The apparatus according to claim 7 further comprisinga light source to illuminate the tag labeled sample.
 9. The apparatusaccording to claim 8 wherein the light source is a broad spectrum lightsource.
 10. The apparatus according to claim 8 further comprising alight source filter configured to be optically coupled between the lightsource and the tag labeled sample wherein the light source filter isconfigured to only substantially allow light waves having an excitationwavelength corresponding to the tag labeled sample to reach the taglabeled sample.
 11. The apparatus according to claim 7 furthercomprising a sensor filter optically coupled between the two dimensionalCCD sensor and the lens wherein the sensor filter is configured to onlysubstantially allow light waves emitted from the tag labeled sample toreach the CCD sensor.
 12. A system configured to detect and locatefluorescently labeled samples on a biochip, the biochip having aplurality of samples, the system comprising: a. a light sourceconfigured to simultaneously illuminate all the fluorescently labeledsamples; b. a two dimensional CCD sensor optically coupled to the lightsource and configured for concurrently detecting and locating emittedlight from the fluorescently labeled samples on the biochip; and c. alens optically coupled between the light source and the two dimensionalCCD sensor and configured to appropriately magnify the biochip onto thetwo dimensional CCD sensor.
 13. A system configured to detect and locatea first set of samples labeled by a first fluorescent tag and a secondset of samples labeled by a second fluorescent tag, the systemcomprising: a. a light source configured to simultaneously illuminateall the flourescently labeled samples; b. a two dimensional CCD sensoroptically coupled to the light source and configured for concurrentlydetecting and locating a first emitted light from the first set ofsamples and a second emitted light from the second set of samples; c. alens optically coupled between the light source and the two dimensionalCCD sensor and configured to transmit the first emitted light and thesecond emitted light to the two dimensional CCD sensor; d. a first lightsource filter selectively and optically coupled to the light source andconfigured for substantially only transmitting a first illuminatinglight to the first set of samples to excite the first set of samples; e.a first sensor filter selectively and optically coupled to the twodimensional CCD sensor and configured for substantially onlytransmitting the first emitted light to the two dimensional CCD sensor;f. a second light source filter selectively and optically coupled to thelight source and configured for substantially only transmitting a secondilluminating light to the second set of samples to excite the second setof samples; and g. a second sensor filter selectively and opticallycoupled to the two dimensional CCD sensor and configured forsubstantially only transmitting the second emitted light to the twodimensional CCD sensor.
 14. A method of detecting and locating a firstsample labeled by a first fluorescent tag and a second sample labeled bya second fluorescent tag wherein the first sample and the second sampleare on a biochip, the method comprising the following steps: a.selectively exciting the first sample by substantially directing onlylight having a first excitation wavelength for exciting the firstfluorescent tag from a broad spectrum light source to the first sample;b. selectively detecting the first sample during the step of excitingthe first sample by substantially directing only light having a firstemission wavelength emitted by and from the first sample to a twodimensional CCD sensor; c. selectively exciting the second sample bysubstantially directing only light having a second excitation wavelengthfor exciting the second fluorescent tag from the broad spectrum lightsource to the second sample; and d. selectively detecting the secondsample during the step of exciting the second sample by substantiallydirecting only light having a second emission wavelength emitted by andfrom the second sample to the two dimensional CCD sensor.
 15. A methodof detecting and locating a sample labeled with a fluorescent tag, themethod comprising the following steps: a. illuminating the sample with alight source; b. focussing an emitted light from the sample via a lenswherein the lens is located at a distance that is less than 6.0 inchesfrom the sample; and c. detecting the emitted light from the sample viaa CCD sensor.
 16. The method according to claim 15 further comprisinginserting a light source filter adjacent to the light source wherein thelight source filter is configured to substantially block light wavesthat have wavelengths outside an excitation wavelength range of thefluorescent tag from reaching the sample.
 17. The method according toclaim 15 further comprising inserting a sensor filter adjacent to theCCD sensor wherein the sensor filter is configured to substantiallyblock light waves that have wavelengths outside an emission wavelengthrange of the fluorescent tag from reaching the CCD sensor.
 18. Themethod according to claim 15 wherein the CCD sensor comprises a twodimensional array of charge coupled devices.
 19. The method according toclaim 15 wherein the light source is a broad spectrum light source.